A data access method for accessing a flash memory storage system, a storage system and a controller using the same are provided. A flash memory has a plurality of physical blocks, which are grouped into a system area, a data area, and a spare area. One or more variable tables are established to record transient information of each set of mother-child blocks of the data area and the spare area. The number of the variable table could be adjusted adaptively according to time required for writing the variable table into the system area, such that an overall data access efficiency of the flash memory storage system is enhanced.